CHANGES IN VERSION 1.5.2
------------------------
UPDATES
o fixed trace names, cleanup
o updated the code downloading SDRFs to rename seq.srdf.txt to .sdrf.txt
o unified the functions providing default options
o exposed the options that are used in the process
o changed errors to warnings where process can still be completed
o fixed improper tools detection on the external R Cloud, added
detection using elements in PATH.
o simplified setting of tools options, removed the need to invoke
initEnvironmentVariables after the options are set, made it automatic
o updated help pages
o composed all options related pages into "package options"
page and "processing options" page. Exposed all options.
o removed the initEnvironmentVariables
o removed outdated references
CHANGES IN VERSION 1.5.1
------------------------
UPDATES
o improved error handling within the ArrayExpressHTS
o added stop.on.warnings that allows detection of possible failures
earlier. However if used it would narrow the amount of experiments
that can be successfully processed.
o added log.error instead of log.info where necessary
o reorganised pipeline options, made them visible to users in the command syntax.
o reorganised R Cloud parameters into a single set of visible/usable options
o made the pipeline automatically detect "Organism" from SDRF and filter using
a selected value.
o reworked reading from SDRF to cover most of the "flexible formatting" cases
o improved creation of R Cloud computation cluster, widened usage of retries.
o added proper functions to work with environment variables
o updated package help pages
o updated the annotation processing following Ensembl update.
o updated help pages, descriptions and references
o updated package vignette documentation
o slightly reorganised the structure of the document
o rewritten some sections
o added a few new sections
o added examples where needed
o reimplemented problematic searching and downloading of .seq.sdrf.txt files
o fixed problematic handling of "NA" or "missing" nominal length values from ENA
o made a number of reference preparation tasks be able to run in parallel and
not affect each other.
o fixed the "count" method to properly read fields of bam files
CHANGES IN VERSION 1.3.1
------------------------
NEW FEATURES
o Added test dataset, which is a cut version of E-GEOD-16190 experiment
o Added normalization of the reference folder
o Added automatic fixing of reference .fai index, namely duplicated chromosome entries
o Added automatic detection of quality scale where possible
o Added and option to specify quality scale for custom experiments
o Performed performance and memory optimization
o Removed options$reference_version. Since the pipeline allows processing of
multi-species datasets, a single version cannot fit into multiple organism
paradigm. The pipeline always runs on the latest version of reference.
Support for custom versions can be added upon request.
o Added memory monitoring
BUG FIXES
o Fixes to accommodate changes in Ensembl interfaces, required for
preparation of reference and annotation data.
o Fixes to accommodate changes in ENA interfaces, required for querying
metadata & downloading datasets for ArrayExpress experiments.
o Fixed examples in prepareReference help page
o Fixed ArrayExpressHTSFastQ scenario without .sdrf
o Fixed production of final alignment report
CHANGES IN VERSION 1.3.0
------------------------
o No changes. Version changed due to package propagation.
CHANGES IN VERSION 1.0.1
------------------------
NEW FEATURES
o added prepareAnnotation and prepareReference functions
o reworked the discovery of reference data
o updated the package after upgrading R and related packages on the EBI R-Cloud
BUG FIXES
o Fixed computation of insert size for paired end experiments
o Fixed fltbam tool that was not part of the pipeline and could not be invoked
o Fixed plot_scatter_samples calling to_expressionset with wrong argumenta
o Fixed problems with graphics after upgrade of R and graphics subsystem